2019 Model Metrics Challenge Summary Statistics
Challenge Target
| T1 Apoferritin 1.8 Å (EMD-20026) | 16 |
| T2 Apoferritin 2.3 Å (EMD-20027) | 15 |
| T3 Apoferritin 3.1 Å (EMD-20028) | 15 |
| T4 Alcohol Dehydrogenase 2.9 Å (EMD-0406) | 17 |
Which target map was used for (final) fitting?
| primary map of the EMDB entry (emd_#####.map) | 42 |
| unsharpened/unmodified map from reconstruction software (emd_#####_additional_#.map) | 16 |
| half-map 1 for the FSC calculation (emd_#####_half_map_1.map) | 5 |
Did you modify the map?
| yes | 21 |
| no | 42 |
Map preparation procedures used (answered by
21 responding yes to "did you modify the map?")
| yes | no | |
|---|---|---|
| low pass filter | 9 | 12 |
| high pass filter | 4 | 17 |
| local normalization | 4 | 17 |
| segmentation | 5 | 16 |
| applied a mask | 10 | 11 |
| sharpened w/ constant B-value | 12 | 9 |
| sharpened w/ variable B-value | 4 | 17 |
| converted to structure factors | 11 | 10 |
Modelling Category
| Created an ab initio model | 51 |
| Optimized a known model | 12 |
Effort type
| fully automated | 22 |
| partially automated, some manual steps | 41 |
| manual | 0 |
Refinement space
| real | 51 |
| reciprocal | 12 |
Inclusion of H-atoms in Model
| yes | 27 |
| no | 37 |
Final model refinement (choose one)
| ARP/wARP/refmac | 8 |
| Chimera | 10 |
| COOT | 1 |
| CDMD | 4 |
| MDFF | 4 |
| pathwalker | 2 |
| phenix | 13 |
| refmac | 4 |
| rosetta | 16 |
| VMD | 1 |
All modelling software used (indicate all used)
| ARP/wARP | 8 |
| Buccaneer | 4 |
| Chimera | 35 |
| COOT | 19 |
| CDMD | 4 |
| direX | 3 |
| mainmast | 10 |
| MDFF | 10 |
| pathwalker | 2 |
| phenix | 16 |
| pymol | 4 |
| refmac | 12 |
| rosetta | 17 |
| situs | 1 |
| TEMPy | 4 |
| VMD | 4 |
Target criteria used to identify model
improvements (indicate all used)
| map vs. model correlation coefficient | 28 |
| map vs. model FSC curve | 19 |
| energy function | 25 |
| cross-validation procedure | 17 |
| Other (additional reported criteria listed below) | 24 |
| --Reciprocal Space Target (refmac) | 8 |
| --EMRinger | 6 |
| --geometry (e.g. molprobity) | 6 |
| --phenix cryo-EM tools | 4 |
| --Segment-based Mander's overlap coefficient | 4 |
| --Q-score | 1 |
Atomic Displacement (B)
| Type of B factor Treatment | All targets | T1 | T2 | T3 | T4 |
|---|---|---|---|---|---|
| single overall B value applied to entire model | 5 | 1 | 1 | 1 | 2 |
| grouped B (segments) | 3 | 1 | 1 | 1 | 0 |
| grouped B (per residue) | 6 | 1 | 1 | 2 | 2 |
| individual B for each atom | 23 | 6 | 6 | 6 | 5 |
| none | 30 | 8 | 7 | 6 | 9 |
Was the map scale (voxel size) adjusted during the modelling process?
| no | 63 |
Validation Checks
| yes | no | |
|---|---|---|
| internal model consistency | 60 | 3 |
| fit of model to the target map | 60 | 3 |
| fit of model to map other than target (cross-validation) | 25 | 38 |